I think the trouble with nut butter is the same with nuts in general. Nuts attract mold. The nuts used in processed nut butters could have been sitting around for a long time before they were made into butter. This is a problem with a lot of packaged foods, which is why fresh is the way to go when on the diet.
The best way to know if the butters bother you is to stop eating them for about a week and see how you feel. Then, try them again by themselves and see how you react. This assumes you are following the diet strictly though. If you frequently break the diet, it may be difficult to tell what's causing a particular reaction.